We develop an efficient alternating framework for learning a generalized version of Factorization Machine (gFM) on steaming data with provable guarantees. When the instances are sampled from $d$ dimensional random Gaussian vectors and the target second order coefficient matrix in gFM is of rank $k$, our algorithm converges linearly, achieves $O(\epsilon)$ recovery error after retrieving $O(k^{3}d\log(1/\epsilon))$ training instances, consumes $O(kd)$ memory in one-pass of dataset and only requires matrix-vector product operations in each iteration. The key ingredient of our framework is a construction of an estimation sequence endowed with a so-called Conditionally Independent RIP condition (CI-RIP). As special cases of gFM, our framework can be applied to symmetric or asymmetric rank-one matrix sensing problems, such as inductive matrix completion and phase retrieval.

The development of deep learning approaches for modeling these multifactorial effects of GVs is still in its nascent stages, primarily due to the lack of comprehensive datasets that capture the intricate relationships between GVs and their downstream effects on complex traits.

Inspired by multi-modal models that align different modalities with natural language, the text has recently been adopted to provide a unified feature space for diverse graphs.

Inspired by the success of foundation models in applications such as ChatGPT, as graph data has been ubiquitous, one can envision the far-reaching impacts that can be brought by Graph Foundation Models (GFMs) with broader applications in the areas such as scientific research, social network analysis, drug discovery, and e-commerce. Despite the significant progress of pre-trained graph neural networks, there haven't been GFMs that can achieve desired performance on various graph-learning-related tasks. Building GFMs may rely on a vocabulary that encodes transferable patterns shared among different tasks and domains. Unlike image and text, defining such transferable patterns for graphs remains an open question. In this paper, we aim to bridge this gap by rethinking the transferable patterns on graphs as computation trees -- i.e., tree structures derived from the message-passing process. Based on this insight, we propose a cross-task, cross-domain graph foundation model named GFT, short for Graph Foundation model with transferable Tree vocabulary. By treating computation trees as tokens within the transferable vocabulary, GFT improves model generalization and reduces the risk of negative transfer. The theoretical analyses and extensive experimental studies have demonstrated the transferability of computation trees and shown the effectiveness of GFT across diverse tasks and domains in graph learning.

Accurate perception of the vehicle's 3D surroundings, including fine-scale road geometry, such as bumps, slopes, and surface irregularities, is essential for safe and comfortable vehicle control. However, conventional monocular depth estimation often oversmooths these features, losing critical information for motion planning and stability. To address this, we introduce Gamma-from-Mono (GfM), a lightweight monocular geometry estimation method that resolves the projective ambiguity in single-camera reconstruction by decoupling global and local structure. GfM predicts a dominant road surface plane together with residual variations expressed by gamma, a dimensionless measure of vertical deviation from the plane, defined as the ratio of a point's height above it to its depth from the camera, and grounded in established planar parallax geometry. With only the camera's height above ground, this representation deterministically recovers metric depth via a closed form, avoiding full extrinsic calibration and naturally prioritizing near-road detail. Its physically interpretable formulation makes it well suited for self-supervised learning, eliminating the need for large annotated datasets. Evaluated on KITTI and the Road Surface Reconstruction Dataset (RSRD), GfM achieves state-of-the-art near-field accuracy in both depth and gamma estimation while maintaining competitive global depth performance. Our lightweight 8.88M-parameter model adapts robustly across diverse camera setups and, to our knowledge, is the first self-supervised monocular approach evaluated on RSRD.

Genomic Foundation Models (GFMs), such as Evolutionary Scale Modeling (ESM), have demonstrated significant success in variant effect prediction. However, their adversarial robustness remains largely unexplored. To address this gap, we propose SafeGenes: a framework for Secure analysis of genomic foundation models, leveraging adversarial attacks to evaluate robustness against both engineered near-identical adversarial Genes and embedding-space manipulations. In this study, we assess the adversarial vulnerabilities of GFMs using two approaches: the Fast Gradient Sign Method (FGSM) and a soft prompt attack. FGSM introduces minimal perturbations to input sequences, while the soft prompt attack optimizes continuous embeddings to manipulate model predictions without modifying the input tokens. By combining these techniques, SafeGenes provides a comprehensive assessment of GFM susceptibility to adversarial manipulation. Targeted soft prompt attacks induced severe degradation in MLM-based shallow architectures such as ProteinBERT, while still producing substantial failure modes even in high-capacity foundation models such as ESM1b and ESM1v. These findings expose critical vulnerabilities in current foundation models, opening new research directions toward improving their security and robustness in high-stakes genomic applications such as variant effect prediction.

Floods are among the most damaging weather-related hazards, and in 2024, the warmest year on record, extreme flood events affected communities across five continents. Earth observation (EO) satellites provide critical, frequent coverage for mapping inundation, yet operational accuracy depends heavily on labeled datasets and model generalization. Recent Geospatial Foundation Models (GFMs), such as ESA-IBM's TerraMind, offer improved generalizability through large-scale self-supervised pretraining, but their performance on diverse global flood events remains poorly understood. We fine-tune TerraMind for flood extent mapping using FloodsNet, a harmonized multimodal dataset containing co-located Sentinel-1 (Synthetic Aperture Radar, SAR data) and Sentinel-2 (optical) imagery for 85 flood events worldwide. We tested four configurations (base vs. large models; frozen vs. unfrozen backbones) and compared against the TerraMind Sen1Floods11 example and a U-Net trained on both FloodsNet and Sen1Floods11. The base-unfrozen configuration provided the best balance of accuracy, precision, and recall at substantially lower computational cost than the large model. The large unfrozen model achieved the highest recall. Models trained on FloodsNet outperformed the Sen1Floods11-trained example in recall with similar overall accuracy. U-Net achieved higher recall than all GFM configurations, though with slightly lower accuracy and precision. Our results demonstrate that integrating multimodal optical and SAR data and fine-tuning a GFM can enhance near-real-time flood mapping. This study provides one of the first global-scale evaluations of a GFM for flood segmentation, highlighting both its potential and current limitations for climate adaptation and disaster resilience.

Graph Foundation Models (GFMs) are pre-trained on diverse source domains and adapted to unseen targets, enabling broad generalization for graph machine learning. Despite that GFMs have attracted considerable attention recently, their vulnerability to backdoor attacks remains largely underexplored. A compromised GFM can introduce backdoor behaviors into downstream applications, posing serious security risks. However, launching backdoor attacks against GFMs is non-trivial due to three key challenges. (1) Effectiveness: Attackers lack knowledge of the downstream task during pre-training, complicating the assurance that triggers reliably induce misclassifications into desired classes. (2) Stealthiness: The variability in node features across domains complicates trigger insertion that remains stealthy. (3) Persistence: Downstream fine-tuning may erase backdoor behaviors by updating model parameters. To address these challenges, we propose GFM-BA, a novel Backdoor Attack model against Graph Foundation Models. Specifically, we first design a label-free trigger association module that links the trigger to a set of prototype embeddings, eliminating the need for knowledge about downstream tasks to perform backdoor injection. Then, we introduce a node-adaptive trigger generator, dynamically producing node-specific triggers, reducing the risk of trigger detection while reliably activating the backdoor. Lastly, we develop a persistent backdoor anchoring module that firmly anchors the backdoor to fine-tuning-insensitive parameters, enhancing the persistence of the backdoor under downstream adaptation. Extensive experiments demonstrate the effectiveness, stealthiness, and persistence of GFM-BA.

We develop an efficient alternating framework for learning a generalized version of Factorization Machine (gFM) on steaming data with provable guarantees. When the instances are sampled from $d$ dimensional random Gaussian vectors and the target second order coefficient matrix in gFM is of rank $k$, our algorithm converges linearly, achieves $O(\epsilon)$ recovery error after retrieving $O(k^{3}d\log(1/\epsilon))$ training instances, consumes $O(kd)$ memory in one-pass of dataset and only requires matrix-vector product operations in each iteration. The key ingredient of our framework is a construction of an estimation sequence endowed with a so-called Conditionally Independent RIP condition (CI-RIP). As special cases of gFM, our framework can be applied to symmetric or asymmetric rank-one matrix sensing problems, such as inductive matrix completion and phase retrieval.

FMs have been found successful in many applications, such as recommendation systems [Rendle et al., 2011] and text retrieval [Hong et al., 2013].